Genomes were obtained from the National Center for Biotechnology Information (NCBI) RefSeq [1]} database (accessed on 2019 March 20). We first obtained the `representative,' `reference,' `complete,' `contig,' and `scaffold' sets and reduced these to a set of genus-level representatives using the following sampling procedure. We first selected a random representative genome for all unique genera in the combined `representative' and `reference' sets. Novel genera in the remaining RefSeq categories, that were not already represented in the `reference' and `representative' sets, were then appended to the set in the same way, for a total \(N = 2,621\)  genomes. Metabolic models were constructed for the selected genome assemblies using the CarveMe reconstruction algorithm [2]}, that starts with a universal bacterial metabolic model comprising known biochemical reactions in the BiGG Models [3]} database and generates genome-specific reaction sets by paring those without genomic support. Finally, metabolic models' cytoplasmic compartments were summarized as metabolic networks — directed graphs in which nodes are chemical metabolite compounds and directed edges link substrates to products [4]}.
